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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.27

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/taxtriage analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2026-01-22, 15:36 UTC based on data in: /Users/user/taxtriage/work/8f/dfae9ad743eee49c0ede7ae1e03f5e

        Confidence Metrics

        Confidence values for all organisms.
        ★ Indicates a high consequence pathogen.

        Showing 34/34 rows and 18/34 columns.
        IndexSpecimen IDDetected OrganismTASS ScoreMicrobial CategorySample Type% ReadsCoverageMean DepthMean BaseQMean MapQTaxonomic ID #IsAnnotatedHHS Percentileindex# Reads Aligned% Aligned ReadsAnnClassHigh ConsequenceStatusGini CoefficientMean CoverageisSpeciesPathogenic Subsp/StrainsK2 ReadsParent K2 ReadsMapQ ScoreDisparity ScoreMinhash ScoreDiamond IdentityK2 Disparity ScoreSiblings scoreBreadth Weight ScoreMicrobeRT ModelGroup
        0
        Miseq_Run_A
        ★ Monkeypox virus
        1.0
        Primary
        nasal
        1.1
        0.81
        0.00
        32.78
        56.58
        10244
        Yes
        100.00
        13
        1278
        1.1
        Direct
        True
        established
        1.0
        0.8
        False
        Zaire-96-I-16 (1.1%)
        654.0
        0
        1.0
        0.9
        1.0
        0.0
        0.0
        0.0
        1.0
        Unknown
        1
        Miseq_Run_A
        ★ Listeria monocytogenes EGD-e°
        1.0
        Primary
        nasal
        8.2
        0.59
        0.00
        32.83
        57.90
        169963
        Yes
        100.00
        8
        9649
        8.2
        Derived
        True
        established
        1.0
        0.6
        False
        4891.0
        0
        1.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        2
        ONT_Run_A
        ★ Listeria monocytogenes EGD-e
        1.0
        Primary
        stool
        6.7
        0.30
        0.00
        13.96
        58.62
        169963
        Yes
        100.00
        12
        201
        3.7
        Direct
        True
        established
        1.0
        0.3
        False
        EGD-e (3.7%)
        199.0
        0
        1.0
        0.9
        1.0
        0.0
        0.0
        0.0
        0.8
        Unknown
        3
        Miseq_Run_A
        ★ Severe acute respiratory syndrome coronavirus 2°
        1.0
        Primary
        nasal
        0.1
        0.64
        0.00
        32.95
        59.77
        2697049
        Yes
        100.00
        15
        100
        0.1
        Derived
        True
        established
        1.0
        0.6
        False
        50.0
        0
        1.0
        0.5
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        4
        ONT_Run_A
        ★ Salmonella enterica subsp. enterica serovar Typhimurium str. LT2°
        0.9
        Primary
        stool
        3.4
        0.09
        0.00
        13.97
        4.07
        99287
        No
        100.00
        2
        103
        1.9
        Derived
        True
        1.0
        0.5
        False
        84.0
        0
        0.6
        0.9
        1.0
        0.0
        1.0
        0.0
        0.6
        Unknown
        5
        ONT_Run_A
        ★ Salmonella enterica subsp. enterica serovar Typhimurium°
        0.9
        Primary
        stool
        3.3
        0.08
        0.00
        13.97
        0.00
        90371
        No
        100.00
        14
        99
        1.9
        Derived
        True
        1.0
        0.5
        False
        84.0
        0
        0.0
        0.9
        1.0
        0.0
        1.0
        0.0
        0.6
        Unknown
        6
        ONT_Run_A
        ★ Salmonella enterica subsp. enterica serovar Typhi str. Ty2°
        0.9
        Primary
        stool
        1.1
        0.05
        0.00
        0.00
        0.00
        209261
        No
        100.00
        3
        32
        0.6
        Derived
        True
        1.0
        0.1
        False
        0.0
        0
        0.0
        0.7
        1.0
        0.0
        0.0
        0.0
        0.6
        Unknown
        7
        ONT_Run_A
        ★ Listeria monocytogenes serotype 4b str. F2365°
        0.7
        Primary
        stool
        0.5
        0.02
        0.00
        0.00
        0.00
        265669
        No
        100.00
        5
        14
        0.2
        Derived
        True
        0.8
        0.0
        False
        0.0
        0
        0.0
        0.4
        1.0
        0.0
        0.0
        0.0
        0.4
        Unknown
        8
        ONT_Run_A
        ★ Salmonella enterica subsp. enterica°
        0.7
        Primary
        stool
        3.5
        0.09
        0.00
        9.32
        1.10
        59201
        No
        100.00
        17
        105
        1.9
        Derived
        True
        0.7
        0.4
        False
        126.0
        0
        0.2
        0.9
        0.8
        0.0
        1.0
        0.0
        0.6
        Unknown
        9
        Miseq_Run_A
        ★ Escherichia coli O157:H7°
        0.6
        Primary
        nasal
        15.1
        0.55
        0.00
        21.74
        14.95
        83334
        Yes
        100.00
        14
        17666
        15.1
        Derived
        True
        established
        0.4
        0.2
        False
        27390.0
        0
        1.0
        1.0
        0.8
        0.0
        1.0
        0.0
        0.9
        Unknown
        10
        Miseq_Run_A
        ★ Listeria monocytogenes serotype 4b str. F2365°
        0.5
        Primary
        nasal
        0.1
        0.01
        0.00
        32.44
        1.37
        265669
        No
        100.00
        3
        101
        0.1
        Derived
        True
        0.5
        0.0
        False
        0.0
        0
        0.3
        0.5
        1.0
        0.0
        0.0
        0.0
        0.3
        Unknown
        11
        ONT_Run_A
        ★ Escherichia coli O157:H7
        0.5
        Primary
        stool
        2.7
        0.09
        0.00
        0.00
        0.00
        83334
        Yes
        100.00
        16
        80
        1.4
        Direct
        True
        established
        0.3
        0.0
        False
        7.1_Anguil (1.5%)
        60.0
        0
        0.0
        0.9
        0.7
        0.0
        1.0
        0.0
        0.6
        Unknown
        12
        Miseq_Run_A
        Pseudomonas aeruginosa PAO1°
        1.0
        Primary
        nasal
        28.8
        0.75
        0.00
        32.85
        30.85
        208964
        No
        100.00
        1
        33763
        28.9
        Derived
        False
        1.0
        0.8
        False
        0.0
        0
        1.0
        1.0
        1.0
        0.0
        0.0
        0.0
        1.0
        Unknown
        13
        ONT_Run_A
        Staphylococcus aureus subsp. aureus NCTC 8325°
        1.0
        Commensal
        stool
        30.2
        0.58
        0.00
        13.95
        57.38
        93061
        No
        100.00
        9
        907
        16.6
        Derived
        False
        1.0
        0.6
        False
        901.0
        0
        1.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        14
        Miseq_Run_A
        Escherichia coli str. K-12 substr. MG1655°
        1.0
        Commensal
        nasal
        13.2
        0.60
        0.00
        32.83
        45.19
        511145
        No
        100.00
        0
        15465
        13.2
        Derived
        False
        1.0
        0.6
        False
        0.0
        0
        1.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        15
        Miseq_Run_A
        Staphylococcus aureus subsp. aureus NCTC 8325°
        1.0
        Commensal
        nasal
        7.6
        0.57
        0.00
        32.79
        48.35
        93061
        No
        100.00
        6
        8915
        7.6
        Derived
        False
        1.0
        0.6
        False
        4687.0
        0
        1.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        16
        Miseq_Run_A
        Human respiratory syncytial virus A°
        1.0
        Primary
        nasal
        0.2
        0.97
        0.00
        32.85
        58.67
        208893
        Yes
        100.00
        12
        201
        0.2
        Derived
        False
        established
        1.0
        1.0
        False
        51.0
        0
        1.0
        0.6
        1.0
        0.0
        1.0
        0.0
        1.0
        Unknown
        17
        ONT_Run_A
        Staphylococcus aureus RF122°
        1.0
        Commensal
        stool
        21.3
        0.43
        0.00
        14.35
        0.00
        273036
        No
        100.00
        6
        638
        11.6
        Derived
        False
        1.0
        0.4
        False
        0.0
        0
        0.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        18
        ONT_Run_A
        Bacillus subtilis subsp. subtilis str. 168°
        1.0
        Commensal
        stool
        29.1
        0.43
        0.00
        13.96
        0.67
        224308
        No
        100.00
        7
        873
        15.9
        Derived
        False
        1.0
        0.4
        False
        873.0
        0
        0.1
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        19
        ONT_Run_A
        Bacillus subtilis BSn5°
        1.0
        Commensal
        stool
        24.2
        0.37
        0.00
        14.01
        0.00
        936156
        No
        100.00
        11
        727
        13.3
        Derived
        False
        1.0
        0.4
        False
        0.0
        0
        0.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        20
        ONT_Run_A
        Bacillus subtilis subsp. subtilis°
        1.0
        Commensal
        stool
        28.9
        0.43
        0.00
        13.95
        0.00
        135461
        No
        100.00
        15
        868
        15.8
        Derived
        False
        1.0
        0.4
        False
        873.0
        0
        0.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.9
        Unknown
        21
        Miseq_Run_A
        Bacillus subtilis subsp. subtilis str. 168°
        1.0
        Commensal
        nasal
        5.5
        0.34
        0.00
        32.80
        1.05
        224308
        No
        100.00
        5
        6475
        5.5
        Derived
        False
        1.0
        0.3
        False
        7000.0
        0
        0.2
        1.0
        1.0
        0.0
        0.0
        0.0
        0.8
        Unknown
        22
        Miseq_Run_A
        Bacillus subtilis subsp. subtilis°
        1.0
        Commensal
        nasal
        5.5
        0.34
        0.00
        32.83
        0.25
        135461
        No
        100.00
        10
        6456
        5.5
        Derived
        False
        1.0
        0.3
        False
        7000.0
        0
        0.1
        1.0
        1.0
        0.0
        0.0
        0.0
        0.8
        Unknown
        23
        ONT_Run_A
        Limosilactobacillus fermentum°
        0.9
        Unknown
        stool
        5.2
        0.27
        0.00
        13.95
        21.86
        1613
        No
        100.00
        8
        157
        2.9
        Derived
        False
        1.0
        0.3
        False
        198.0
        0
        1.0
        0.9
        1.0
        0.0
        0.0
        0.0
        0.8
        Unknown
        24
        Miseq_Run_A
        Pseudomonas aeruginosa PA1°
        0.9
        Primary
        nasal
        6.6
        0.23
        0.00
        32.68
        0.16
        1279007
        No
        100.00
        9
        7765
        6.6
        Derived
        False
        1.0
        0.2
        False
        20812.0
        0
        0.0
        1.0
        1.0
        0.0
        0.0
        0.0
        0.8
        Unknown
        25
        Miseq_Run_A
        human respiratory syncytial virus B
        0.9
        Primary
        nasal
        0.0
        0.58
        0.00
        32.20
        58.24
        11250
        Yes
        100.00
        11
        50
        0.0
        Derived
        False
        established
        1.0
        0.6
        False
        76.0
        0
        1.0
        0.3
        1.0
        0.0
        1.0
        0.0
        0.9
        Unknown
        26
        ONT_Run_A
        Escherichia coli str. K-12 substr. MG1655°
        0.9
        Commensal
        stool
        4.5
        0.17
        0.00
        13.96
        59.75
        511145
        No
        100.00
        0
        134
        2.4
        Derived
        False
        1.0
        0.2
        False
        0.0
        0
        1.0
        0.9
        1.0
        0.0
        0.0
        0.0
        0.7
        Unknown
        27
        ONT_Run_A
        Enterococcus faecalis EnGen0336°
        0.9
        Commensal
        stool
        3.0
        0.16
        0.00
        13.97
        60.00
        1169293
        No
        100.00
        4
        90
        1.6
        Derived
        False
        1.0
        0.7
        False
        0.0
        0
        1.0
        0.9
        1.0
        0.0
        0.0
        0.0
        0.7
        Unknown
        28
        Miseq_Run_A
        Bacillus subtilis BSn5°
        0.9
        Commensal
        nasal
        0.9
        0.06
        0.00
        32.86
        0.95
        936156
        No
        100.00
        7
        1043
        0.9
        Derived
        False
        1.0
        0.1
        False
        0.0
        0
        0.2
        0.9
        1.0
        0.0
        0.0
        0.0
        0.6
        Unknown
        29
        Miseq_Run_A
        Staphylococcus aureus RF122°
        0.9
        Commensal
        nasal
        0.4
        0.04
        0.00
        32.57
        1.24
        273036
        No
        100.00
        4
        427
        0.4
        Derived
        False
        1.0
        0.0
        False
        0.0
        0
        0.2
        0.8
        1.0
        0.0
        0.0
        0.0
        0.5
        Unknown
        30
        ONT_Run_A
        Saccharomyces cerevisiae S288C
        0.8
        Commensal
        stool
        8.1
        0.10
        0.00
        13.14
        54.18
        559292
        Yes
        100.00
        10
        243
        4.4
        Direct
        False
        established
        0.9
        0.1
        False
        Commensal Listing
        4012.0
        0
        1.0
        1.0
        1.0
        0.0
        1.0
        0.0
        0.7
        Unknown
        31
        ONT_Run_A
        Pseudomonas aeruginosa PAO1°
        0.8
        Primary
        stool
        0.3
        0.02
        0.00
        13.96
        52.25
        208964
        No
        100.00
        1
        8
        0.1
        Derived
        False
        0.9
        0.0
        False
        0.0
        0
        1.0
        0.1
        1.0
        0.0
        0.0
        0.0
        0.4
        Unknown
        32
        ONT_Run_A
        Pseudomonas aeruginosa PA1°
        0.7
        Primary
        stool
        0.2
        0.02
        0.00
        0.00
        0.00
        1279007
        No
        100.00
        13
        7
        0.1
        Derived
        False
        0.9
        0.0
        False
        8.0
        0
        0.0
        0.0
        1.0
        0.0
        0.0
        0.0
        0.4
        Unknown
        33
        Miseq_Run_A
        Neisseria gonorrhoeae°
        0.6
        Primary
        nasal
        6.1
        0.59
        0.00
        16.41
        28.10
        485
        Yes
        100.00
        2
        7123
        6.1
        Derived
        False
        established
        0.5
        0.3
        False
        7200.0
        0
        1.0
        1.0
        0.8
        0.0
        1.0
        0.0
        0.9
        Unknown

        Kraken

        Taxonomic classification using exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.URL: https://ccb.jhu.edu/software/krakenDOI: 10.1186/gb-2014-15-3-r46

        Top taxa

        The number of reads falling into the top 15 taxa across different ranks.

        To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 15 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

        The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

        The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 15 taxa shown + unclassified. This should cover all taxa not in the top 15, +/- any rounding errors.

        Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

        Created with MultiQC

        fastp

        Version: 0.23.2

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        FastQC

        Version: 0.11.9

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        2 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/0 rows.
        Overrepresented sequence

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Samtools

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Coverage: global stats

        Stats parsed from samtools coverage output, and summarized (added up or weighted-averaged) across all regions.

        Showing 2/2 rows and 6/6 columns.
        Sample NameReadsBasesCoverageMean depthMean BQMean MQ
        Miseq_Run_A
        0.1M
        20.2Mb
        40.8%
        0.6x
        32.7
        22.5
        ONT_Run_A
        0.0M
        8.0Mb
        9.6%
        0.1x
        10.6
        23.1

        Coverage: stats per region

        Per-region stats parsed from samtools coverage output.

        Created with MultiQC

        Metadata

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/taxtriage

        Core Nextflow options

        runName
        naughty_gauss
        containerEngine
        docker
        launchDir
        /Users/user/taxtriage
        workDir
        /Users/user/taxtriage/work
        projectDir
        /Users/user/taxtriage
        userName
        user
        profile
        test,docker
        configFiles
        /Users/user/taxtriage/nextflow.config

        Input/output options (Required)

        input
        examples/Samplesheet_simulated.csv
        db
        /Users/user/Desktop/mytax/test_metagenome
        outdir
        test_output

        Metagenomics Parameters

        top_per_taxa
        10239:10:S 2:10:S
        download_db
        true
        taxtab
        default
        remove_commensal
        true
        top_hits_count
        10
        k2_minimum_hit_groups
        3

        Alignment

        split_prefix
        N/A
        min_conf
        0.40
        gini_weight
        0.71
        breadth_weight
        0.24
        minhash_weight
        0.05
        mapq_weight
        N/A
        disparity_score_weight
        N/A
        hmp_weight
        N/A
        dispersion_factor
        0.55
        reward_factor
        4
        min_reads_align
        1
        zscore_accepted
        1.5
        minmapq
        5
        mmap2_fraction_filter
        0.0009
        igenomes_base
        https://ngi-igenomes.s3.eu-west-1.amazonaws.com/igenomes
        distributions
        N/A

        Skip Steps

        ignore_missing
        true
        show_potentials
        true
        show_commensals
        true
        show_unidentified
        true

        General Info

        validate_params
        true
        max_cpus
        2
        max_memory
        7.GB
        max_time
        10.h
        default_download
        true
        config_profile_name
        Test profile
        config_profile_description
        Minimal test dataset to check pipeline function

        NanoStat

        Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).URL: https://github.com/wdecoster/nanostat; https://github.com/wdecoster/nanoplotDOI: 10.1093/bioinformatics/bty149

        Programs are part of the NanoPack family for summarising results of sequencing on Oxford Nanopore methods (MinION, PromethION etc.)

        Summary Statistics (FASTQ)

        Showing 1/1 rows and 5/7 columns.
        Sample NameMedian lengthMean lengthRead N50Median QualMean Qual# Reads (K)Total Bases (Mb)
        ONT_Run_A
        3356bp
        4065bp
        5203bp
        9.0
        8.6
        3.0K
        12.2Mb

        Reads by quality

        Read counts categorised by read quality (Phred score).

        Sequencing machines assign each generated read a quality score using the Phred scale. The phred score represents the liklelyhood that a given read contains errors. High quality reads have a high score.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        FastQCFastQC0.11.9
        NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BEDTOOLS_GENOMECOVERAGEbedtools2.31.1)
        NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGNminimap22.24-r1122
        NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_COVERAGEsamtools1.19.2
        NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_HIST_COVERAGEsamtools1.19.2
        NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_INDEXsamtools1.17
        NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQCfastqc0.11.9
        fastpfastp0.23.2